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Divergence (dXY) of Introgressed Regions vs. Genome-Wide Background

Figure 1. Distribution of mean absolute nucleotide divergence for introgression tracts and species tree tracts by PhyloNet-HMM posterior probability threshold (90%, 80%)

Figure 1. Distribution of mean absolute nucleotide divergence for introgression tracts and species tree tracts by PhyloNet-HMM posterior probability threshold (90%, 80%)

Shaprio-Wilk tests and QQ Plots

Shapiro Test H0: sample is normally distributed

Introgression Tracts: 90% posterior probability threshold

## Shapiro-Wilk test p-value =  0.519
Figure 2. qqplot for mean dXY distribution for introgression tracts at the 90% threshold

Figure 2. qqplot for mean dXY distribution for introgression tracts at the 90% threshold

Species Tree Tracts: 90% posterior probability threshold

## Shapiro-Wilk test p-value =  0.304
Figure 3. qqplot for mean dXY distribution for species tree tracts at the 90% threshold

Figure 3. qqplot for mean dXY distribution for species tree tracts at the 90% threshold

Introgression Tracts: 80% posterior probability threshold

## Shapiro-Wilk test p-value =  0.274
Figure 4. qqplot for mean dXY distribution for introgression tracts at the 80% threshold

Figure 4. qqplot for mean dXY distribution for introgression tracts at the 80% threshold

Species Tree Tracts: 80% posterior probability threshold

## Shapiro-Wilk test p-value =  0.58
Figure 5. qqplot for mean dXY distribution for species tree tracts at the 80% threshold

Figure 5. qqplot for mean dXY distribution for species tree tracts at the 80% threshold

Homogeneity of variances

Tract Type Posterior Probability Standard Deviation Variance
introgression_tract probability_90 0.00138137 0.00000191
species_tree_tract probability_90 0.00160160 0.00000257
introgression_tract probability_80 0.00064030 0.00000041
species_tree_tract probability_80 0.00065455 0.00000043

F-test to assess homogeneity of variances for dXY between introgression tracts and species tree tracts

F Test H0: Ratio of variances is equal

Posterior Probability Variance Ratio p Confidence Interval
90% 0.744 0.000 [0.657, 0.842]
80% 0.957 0.487 [0.845, 1.083]
log(90%) 1.101 0.129 [0.972, 1.246]
log(80%) 1.319 0.000 [1.165, 1.493]

Welch Two Sample t-test

Posterior Probability t df p Confidence Interval
90% -131.454 1955.819 0 [-0.0089, -0.0087]
80% -258.742 1998.000 0 [-0.0075, -0.0074]

Figure for manuscript

Figure 6. Distribution of mean absolute nucleotide divergence for introgression tracts and species tree tracts by PhyloNet-HMM posterior probability threshold (90%, 80%)

Figure 6. Distribution of mean absolute nucleotide divergence for introgression tracts and species tree tracts by PhyloNet-HMM posterior probability threshold (90%, 80%)

Gene Density of Introgressed Regions vs. Genome-Wide Background

Figure 7. Distribution of the number of overlapping protein-coding genes per Mb for introgression tracts and species tree tracts by PhyloNet-HMM posterior probability threshold (90%, 80%)

Figure 7. Distribution of the number of overlapping protein-coding genes per Mb for introgression tracts and species tree tracts by PhyloNet-HMM posterior probability threshold (90%, 80%)

Introgression Tract Gene Count: 90% posterior probability threshold

Figure 8. Normal fit of gene counts for introgression tracts at the 90% posterior probability threshold

Figure 8. Normal fit of gene counts for introgression tracts at the 90% posterior probability threshold

Species Tree Tract Gene Count: 90% posterior probability threshold

Figure 9. Normal fit of gene counts for species tree tracts at the 90% posterior probability threshold

Figure 9. Normal fit of gene counts for species tree tracts at the 90% posterior probability threshold

Introgression Tract Gene Count: 80% posterior probability threshold

Figure 10. Normal fit of gene counts for introgression tracts at the 80% posterior probability threshold

Figure 10. Normal fit of gene counts for introgression tracts at the 80% posterior probability threshold

Species Tree Tract Gene Count: 80% posterior probability threshold

Figure 11. Normal fit of gene counts for species tree tracts at the 80% posterior probability threshold

Figure 11. Normal fit of gene counts for species tree tracts at the 80% posterior probability threshold

Normal vs. log normal fit for Gene Counts

Tract Type Posterior Probability Fit aic
Introgression 90% Normal 3533.1
Introgression 90% Log Normal 3546.5
Introgression 80% Normal 2078.2
Introgression 80% Log Normal 2079.2
Species Tree 90% Normal 4702.2
Species Tree 90% Log Normal 4698.8
Species Tree 80% Normal 4702.2
Species Tree 80% Log Normal 4698.8

Homogeneity of variances for Gene Count

Tract Type Posterior Probability Standard Deviation Variance
Introgression 90% 1.4135504 1.998125
Species Tree 90% 2.5362019 6.432320
Introgression 80% 0.6829458 0.466415
Species Tree 80% 1.0332989 1.067707

F-test to assess homogeneity of variances between gene counts for introgression tracts and species tree tracts

F Test H0: Ratio of variances is equal

Posterior Probability Variance Ratio p Confidence Interval
90% 0.311 0.000 [0.274, 0.352]
80% 0.437 0.000 [0.386, 0.495]
log(90%) 0.839 0.006 [0.741, 0.950]
log(80%) 0.795 0.000 [0.702, 0.900]

Welch Two Sample t-test

Posterior Probability t df p Confidence Interval
90% -121.046 1565.035 0 [-11.2942, -10.934]
80% -191.011 1998.000 0 [-7.5583, -7.4047]

Figure for Manuscript

Figure 10. Distribution of gene counts for introgression tracts and species tree tracts by PhyloNet-HMM posterior probability threshold (90%, 80%)

Figure 10. Distribution of gene counts for introgression tracts and species tree tracts by PhyloNet-HMM posterior probability threshold (90%, 80%)

Percent Coding for Introgressed Regions vs. Genome-Wide Background

Introgression Tract Percent Coding: 90% posterior probability threshold

Figure 8. Normal fit of gene counts for introgression tracts at the 90% posterior probability threshold

Figure 8. Normal fit of gene counts for introgression tracts at the 90% posterior probability threshold

Species Tree Tract Percent Coding: 90% posterior probability threshold

Figure 9. Normal fit of gene counts for species tree tracts at the 90% posterior probability threshold

Figure 9. Normal fit of gene counts for species tree tracts at the 90% posterior probability threshold

Introgression Tract Percent Coding: 80% posterior probability threshold

Figure 10. Normal fit of gene counts for introgression tracts at the 80% posterior probability threshold

Figure 10. Normal fit of gene counts for introgression tracts at the 80% posterior probability threshold

Species Tree Tract Percent Coding: 80% posterior probability threshold

Figure 11. Normal fit of gene counts for species tree tracts at the 80% posterior probability threshold

Figure 11. Normal fit of gene counts for species tree tracts at the 80% posterior probability threshold

Homogeneity of variances for Percent Coding

Tract Type Posterior Probability Standard Deviation Variance
Introgression 90% 0.3463958 0.11999004
Species Tree 90% 0.4826987 0.23299805
Introgression 80% 0.2368049 0.05607657
Species Tree 80% 0.1938070 0.03756116

F-test to assess homogeneity of variances between percent coding for introgression tracts and species tree tracts

F Test H0: Ratio of variances is equal

Posterior Probability Variance Ratio p Confidence Interval
90% 0.515 0.000 [0.455, 0.583]
80% 1.493 0.000 [1.319, 1.690]
log(90%) 0.999 0.989 [0.883, 1.131]
log(80%) 1.784 0.000 [1.576, 2.019]

Figure for Manuscript

Figure X. Percentage of coding bases for introgression tracts greater than 10 kb in length and the genome-wide background.

Figure X. Percentage of coding bases for introgression tracts greater than 10 kb in length and the genome-wide background.

Number of Positively Selected Genes for Introgressed Regions vs. Genome-Wide Background

Introgression Tract PSG Count: 90% posterior probability threshold

Figure 8. Normal fit of gene counts for introgression tracts at the 90% posterior probability threshold

Figure 8. Normal fit of gene counts for introgression tracts at the 90% posterior probability threshold

Species Tree Tract PSG Count: 90% posterior probability threshold

Figure 9. Normal fit of gene counts for species tree tracts at the 90% posterior probability threshold

Figure 9. Normal fit of gene counts for species tree tracts at the 90% posterior probability threshold

Introgression Tract PSG Count: 80% posterior probability threshold

Figure 10. Normal fit of gene counts for introgression tracts at the 80% posterior probability threshold

Figure 10. Normal fit of gene counts for introgression tracts at the 80% posterior probability threshold

Species Tree Tract PSG Count: 80% posterior probability threshold

Figure 11. Normal fit of gene counts for species tree tracts at the 80% posterior probability threshold

Figure 11. Normal fit of gene counts for species tree tracts at the 80% posterior probability threshold

Homogeneity of variances for PSG Count

Tract Type Posterior Probability Standard Deviation Variance
Introgression 90% 0.24296527 0.05903212
Species Tree 90% 0.62125698 0.38596023
Introgression 80% 0.08270583 0.00684025
Species Tree 80% 0.25133135 0.06316745

F-test to assess homogeneity of variances between PSG counts for introgression tracts and species tree tracts

F Test H0: Ratio of variances is equal

Posterior Probability Variance Ratio p Confidence Interval
90% 0.153 0.000 [0.135, 0.173]
80% 0.108 0.000 [0.096, 0.123]
log(90%) 0.818 0.002 [0.723, 0.927]
log(80%) 1.420 0.000 [1.254, 1.608]

Welch Two Sample t-test

Posterior Probability t df p Confidence Interval
90% -44.111 1297.606 0 [-0.9719, -0.8891]
80% -133.810 1998.000 0 [-1.136, -1.1032]

dN, dS, dN/dS for Introgressed Regions vs. Genome-Wide Background

Welch Two Sample t-test

Posterior Probability t df p Confidence Interval
90% -65.184 1078.181 0 [-0.1386, -0.1305]
80% -34.513 1998.000 0 [-0.0456, -0.0407]

Figure for Manuscript

Figure X. mean H. pulcherrimus - S. fragilis dN, dS, and dN/dS for introgression tracts greater than 10 kb in length and the genome-wide background.

Figure X. mean H. pulcherrimus - S. fragilis dN, dS, and dN/dS for introgression tracts greater than 10 kb in length and the genome-wide background.